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1455498152
* Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
63 lines
2 KiB
Text
63 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process CNVKIT_BATCH {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0"
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}
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input:
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tuple val(meta), path(tumor), path(normal)
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path fasta
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path targets
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path reference
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.cnn"), emit: cnn, optional: true
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tuple val(meta), path("*.cnr"), emit: cnr, optional: true
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tuple val(meta), path("*.cns"), emit: cns, optional: true
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path "versions.yml" , emit: versions
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script:
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normal_args = normal ? "--normal $normal" : ""
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fasta_args = fasta ? "--fasta $fasta" : ""
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reference_args = reference ? "--reference $reference" : ""
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def target_args = ""
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if (options.args.contains("--method wgs") || options.args.contains("-m wgs")) {
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target_args = targets ? "--targets $targets" : ""
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}
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else {
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target_args = "--targets $targets"
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}
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"""
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cnvkit.py \\
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batch \\
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$tumor \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes ${task.cpus} \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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